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MEDME specifications

Information


Unique identifier OMICS_00614
Name MEDME
Alternative name Modeling Experimental Data with MeDIP Enrichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.40.0
Stability Stable
Requirements
methods, stats, graphics, utils, Biostrings, grDevices, R(>=2.15), BSgenome.Hsapiens.UCSC.hg18, MASS, drc, BSgenome.Mmusculus.UCSC.mm9
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Mattia Pelizzola

Publication for Modeling Experimental Data with MeDIP Enrichment

MEDME citations

 (13)
library_books

Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis

2016
Sci Rep
PMCID: 4944166
PMID: 27411928
DOI: 10.1038/srep29390

[…] een samples, the log2 ratio obtained from raw data values should be normalised. We performed median centering, quantile normalisation and linear smoothing using Bioconductor packages Ringo, Limma and MEDME.From the normalised log2 ratio data, a sliding-window (750 bp) peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to analyse the MeDIP-chip data. A one-sided Kolmog […]

library_books

Alteration of Gene Expression, DNA Methylation, and Histone Methylation in Free Radical Scavenging Networks in Adult Mouse Hippocampus following Fetal Alcohol Exposure

2016
PLoS One
PMCID: 4852908
PMID: 27136348
DOI: 10.1371/journal.pone.0154836

[…] Raw data was extracted as pair files by NimbleScan software. We ArrayStar performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample. From the normalized log2-ratio data, a sliding-window peak-finding algorithm provided by Nimble […]

library_books

DNA methylation is critical for tooth agenesis: implications for sporadic non syndromic anodontia and hypodontia

2016
Sci Rep
PMCID: 4725352
PMID: 26759063
DOI: 10.1038/srep19162

[…] mples, the log2-ratio for arriving at a raw data value should be normalized. We performed median-centering, quantile normalization, and linear smoothing by the bioconductor packages Ringo, limma, and MEDME. After normalization, normalized log2-ratio data were created for each sample. From the normalized log2-ratio data, a sliding-window peak-finding algorithm, provided by NimbleScan v2.5 (Roche-Ni […]

library_books

Epigenetic Alterations in Density Selected Human Spermatozoa for Assisted Reproduction

2015
PLoS One
PMCID: 4692407
PMID: 26709917
DOI: 10.1371/journal.pone.0145585

[…] WI, USA). Raw data was extracted as pair files by NimbleScan software. Median centering, quartile normalization, and linear smoothing were conducted using the Bioconductor packages Ringo, limma, and MEDME, respectively. Peak-finding algorithm is provided by NimbleScan v2.5 (Roche-NimbleGen). A one-sided Kolmogorov-Smirnov (KS) test is applied for peak finding following manufacture’s guide. Peaks […]

library_books

Insights into the origin of DNA methylation differences between monozygotic twins discordant for schizophrenia

2015
PMCID: 4487197
PMID: 26137221
DOI: 10.1186/s40303-015-0013-5

[…] Raw data generated from scans were normalized (log2-ratio). It followed Median centering, quantile normalization and linear smoothing using Bioconductor packages Ringo, limma, and MEDME. The results were used in a sliding-window (750 bp) peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen). A one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether […]

library_books

DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks

2015
BMC Med Genomics
PMCID: 4494167
PMID: 25943100
DOI: 10.1186/s12920-015-0093-1

[…] ll as 22,532 promoters of the RefSeq genes derived from the UCSC RefFlat files. Median-centering, quantile normalization, and linear smoothing was performed by Bioconductor packages Ringo, limma, and MEDME at ArrayStar. Lastly, in order to compare the two groups’ differentially enriched regions the average of the log2-ratio values for each group (i.e. experimental patient [E] and healthy control [ […]

Citations

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MEDME institution(s)
Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA; Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
MEDME funding source(s)
The Yale Spore in Skin Cancer funded by the National Cancer Institute grant number 1 P50 CA121974; the National Library of Medicine grant K22LM009255; the National Cancer Institute grant K22CA123146-2

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